Align Polyol (xylitol):H+ symporter, PLT4 (characterized)
to candidate WP_010537714.1 KCY_RS0114120 MFS transporter
Query= TCDB::Q1XF07 (519 letters) >NCBI__GCF_000226135.1:WP_010537714.1 Length = 309 Score = 139 bits (350), Expect = 1e-37 Identities = 96/320 (30%), Positives = 157/320 (49%), Gaps = 34/320 (10%) Query: 32 YAFACAMLASMTSILLGYDIGVMSGAAIYIKRDLKVSDVKIEILLGIINLYSLIGSGLAG 91 Y +++A++ L GYD V+SG + + ++ ++ +G + S++G AG Sbjct: 9 YLIFLSVVAALGGFLFGYDTAVISGTIAQVSQLFQLDALQQGWYVGCALIGSIVGVLFAG 68 Query: 92 RTSDWIGRRYTIVFAGAIFFVGALLMGFSPNYWFLMFGRFIAGIGIGYALMIAPVYTAEV 151 SD +GR+ T+V + +F AL S ++ L+ R I G+GIG +++P+Y +EV Sbjct: 69 ILSDKLGRKLTMVISAVLFSTSALGCAISADFTQLVIYRIIGGVGIGVVSIVSPLYISEV 128 Query: 152 SPASSRGFLTSFPEVFINGGILLGYISNFA---------------FSKLSLKVGWRMMLG 196 S A RG L S ++ + G L Y+ N+ +K+ + WR MLG Sbjct: 129 SVAQYRGRLVSLYQLAVTVGFLGAYLVNYQLLGYAQSGSQLSIDWLNKIFVTEVWRGMLG 188 Query: 197 VGALPSVILGVGVLAMPESPRWLVMRGRLGDAIKVLNKTSDSPEEAQLRLADIKRAAGIP 256 + LP+V+ + + +PESPRWL+++G+ A+ +L K +S EA +L + Sbjct: 189 MEMLPAVLFFIIIFFIPESPRWLIVKGKEEKAVNILEKIYNSVSEATSQLNE-------- 240 Query: 257 ESCTDDVVEVSKRSTGEGVWKELFLYPTPAIRHIVIAALGIHFFQQASGIDAVVLYSPTI 316 T V+ +S E L P I VI + I Q G++AV+ Y P+I Sbjct: 241 ---TKSVLTSETKS-------EWALLMKPGIFKAVIIGVCIAILGQFMGVNAVLYYGPSI 290 Query: 317 FEKAGIKSDTDKLLATVAVG 336 FE AG+ S D L V VG Sbjct: 291 FENAGL-SGGDSLFYQVLVG 309 Lambda K H 0.323 0.140 0.414 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 389 Number of extensions: 25 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 519 Length of database: 309 Length adjustment: 31 Effective length of query: 488 Effective length of database: 278 Effective search space: 135664 Effective search space used: 135664 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory